Sugarcane has been cultivated as a raw material for sugar or for alcoholic drink. In addition, sugarcane has been used in a variety of industrial fields, including the use as a raw material for biofuel. Under such circumstances, there is a need to develop a method for identifying a sugarcane variety/line in a convenient manner in order to breed sugarcane varieties having desirable characteristics (e.g., sugar content, enhanced vegetative capacity, sprouting capacity, disease resistance, insect resistance, and cold resistance).
The following three ways may be used for identification of a plant variety/line: “characteristics comparison” for comparison of characteristics data, “comparison of cultivation” for comparison of plants cultivated under the same conditions, and “DNA assay” for DNA analysis. There are many problems in line identification with the use of characteristics comparison or comparison of cultivation, including reduction of precision due to differences in cultivation conditions, lengthy duration of field research that requires a number of steps, and the like. In particular, since sugarcane plants are much larger than other graminaceous crops such as rice and maize, it has been difficult to conduct line identification based on field research.
Meanwhile, in the case of sugarcane, the development of genetic marker technology has been delayed because of genomic complexity. Although the USDA reported genotyping with the use of SSR markers (Non Patent Literature 1), the precision of genotyping is low because of the small numbers of markers and polymorphisms in each marker. In addition, the above genotyping is available only for American/Australian varieties and therefore cannot be used for line identification of the major varieties cultivated in Japan, Taiwan, India, and other countries and of useful genetic resources.